The covariance perceptron: A new paradigm for classification and processing of time series in recurrent neuronal networks

Learning in neuronal networks has developed in many directions, in particular to reproduce cognitive tasks like image recognition and speech processing. Implementations have been inspired by stereotypical neuronal responses like tuning curves in the visual system, where, for example, ON/OFF cells fire or not depending on the contrast in their receptive fields. Classical models of neuronal networks therefore map a set of input signals to a set of activity levels in the output of the network. Each category of inputs is thereby predominantly characterized by its mean. In the case of time series, fluctuations around this mean constitute noise in this view. For this paradigm, the high variability exhibited by the cortical activity may thus imply limitations or constraints, which have been discussed for many years. For example, the need for averaging neuronal activity over long periods or large groups of cells to assess a robust mean and to diminish the effect of noise correlations. To reconcile robust computations with variable neuronal activity, we here propose a conceptual change of perspective by employing variability of activity as the basis for stimulus-related information to be learned by neurons, rather than merely being the noise that corrupts the mean signal. In this new paradigm both afferent and recurrent weights in a network are tuned to shape the input-output mapping for covariances, the second-order statistics of the fluctuating activity. When including time lags, covariance patterns define a natural metric for time series that capture their propagating nature. We develop the theory for classification of time series based on their spatio-temporal covariances, which reflect dynamical properties. We demonstrate that recurrent connectivity is able to transform information contained in the temporal structure of the signal into spatial covariances. Finally, we use the MNIST database to show how the covariance perceptron can capture specific second-order statistical patterns generated by moving digits.

The dynamics in cortex is characterized by highly fluctuating activity: Even under the very same experimental conditions the activity typically does not reproduce on the level of individual spikes. Given this variability, how then does the brain realize its quasi-deterministic function? One obvious solution is to compute averages over many cells, assuming that the mean activity, or rate, is actually the decisive signal. Variability across trials of an experiment is thus considered noise. We here explore the opposite view: Can fluctuations be used to actually represent information? And if yes, is there a benefit over a representation using the mean rate? We find that a fluctuation-based scheme is not only powerful in distinguishing signals into several classes, but also that networks can efficiently be trained in the new paradigm. Moreover, we argue why such a scheme of representation is more consistent with known forms of synaptic plasticity than rate-based network dynamics.

Tacit working models of human behavioural change II: Farmers' folk theories of conservation programme design

Community involvement may be essential for conservation programme success. We focus on farmers, asking how and why they believe conservation interventions will work, or not. Here we test models of folk theories of the human motivational factors required for behaviour change, in 3 rural central Chilean communities. We hypothesize that different models will be supported by farmers with different experiences with conservation programmes, and that socioeconomic and production system variation will explain further variation in who supports each working model. We use a multiple methods approach, combining a questionnaire with participant-observation. We find support for three of the working models of human behavioural change, among different socio-economic profiles of farmers. We believe that the schema of working models provides a boundary object to facilitate communication between conservationists and stakeholders, and can help improve conservation project design and implementation.

Hybrid sideways/longitudinal swimming in the monoflagellate Shewanella oneidensis: from aerotactic band to biofilm

Shewanella oneidensis MR-1 are facultative aerobic electroactive bacteria with an appealing potential for sustainable energy production and bioremediation. They gather around air sources, forming aerotactic bands and biofilms. Here, we experimentally follow the evolution of the band around an air bubble, and we find good agreement with the numerical solutions of the pertinent transport equations. Video microscopy reveals a transition between motile and non-motile MR-1 upon oxygen depletion, preventing further development of the biofilm. We discover that MR-1 can alternate between longitudinal fast and sideways slow swimming. The resulting bimodal velocity distributions change in response to different oxygen concentrations and gradients, supporting the biological functions of aerotaxis and confinement.

Interaction of Signaling Lymphocytic Activation Molecule Family 1 (SLAMF1) receptor with Trypanosoma cruzi is strain-dependent and affects NADPH oxidase expression and activity

The receptor Signaling Lymphocyte-Activation Molecule Family 1 (SLAMF1) controls susceptibility to Infection by the lethal Trypanosoma cruzi Y strain. To elucidate whether genetic diversity of the parasite was related with disease susceptibility, we further analyzed the role of SLAMF1 using 6 different Trypanosoma cruzi strains including Y. The interaction of SLAMF1 receptor with T. cruzi was evidenced by fluorescence microscopy, flow cytometry and quantitative PCR. All the strains, except VFRA, showed a decrease in parasite load in infected macrophages in Slamf1^-/- compared to BALB/c. In macrophages gene expression NADPH oxidase (NOX2), and reactive oxygen species (ROS) production increased in Slamf1^-/- compared to BALB/c in 5 out of 6 strains. However, Slamf1^-/-macrophages infected with VFRA strain exhibited a divergent behavior, with higher parasite load, lower NOX2 expression and ROS production compared to BALB/c. Parasitological and immunological studies in vivo with Y strain showed that in the absence of SLAMF1 the immune response protected mice from the otherwise lethal Y infection favoring a proinflammatory response likely involving CD4, CD8, dendritic cells and classically activated macrophages. In the case of VFRA, no major changes were observed in the absence of SLAMF1. Thus, the results suggest that the T. cruzi affects SLAMF1-dependent ROS production, controlling parasite replication in macrophages and affecting survival in mice in a strain-dependent manner. Further studies will focus in the identification of parasite molecules involved in SLAMF1 interaction to explain the immunopathogenesis of the disease.

Chagas disease, caused by Trypanosoma cruzi, is characterized by an acute phase, with low mortality, and after many years without any sign of disease, patients develop a symptomatic chronic phase, characterized by cardiomyopathy and/or digestive mega syndromes. These differences have been attributed to the high genetic variability of this parasite. We have shown that the receptor Signaling Lymphocyte-Activation Molecule Family 1 (SLAMF1) controls susceptibility to Infection by the lethal T. cruzi Y strain. Here we studied in detail the immunopathogenic role of SLAMF1 using 6 genetically diverse strains of T. cruzi using in vitro and in vivo approaches. Our results indicate an important role of SLAMF1 in T. cruzi infection which is parasite strain-dependent. We found that parasites interact with SLAMF1 in macrophages affecting NADPH oxidase (NOX2) expression and reactive oxygen species (ROS) production 5 out of 6 strains tested. Y and VFRA strains showed a divergent behavior in vitro and the role of SLAMF1 in the in vivo infection was also strikingly different. The Y strain caused 70% mortality in BALB/c mice but not in Slamf1^-/- mice. The proinflammatory response was stronger in the last, suggesting that SLAMF1 was repressing protective immune responses of mice infected with the Y strain. In contrast, for VFRA, SLAMF1 deficiency resulted in 100% survival of BALB/c mice, without major changes in the immune response in the absence of SLAMF1. Thus, the results indicate that SLAMF1 receptor interacts with T. cruzi, affecting parasite replication and ROS production in macrophages as well as the adaptive immune response in mice in a parasite strain-dependent manner. Future studies will focus in understanding the immunopathogenic role of SLAMF1 during T. cruzi infection.

Two C-terminal sequence variations determine differential neurotoxicity between human and mouse α-synuclein

BACKGROUND

α-Synuclein (aSyn) aggregation is thought to play a central role in neurodegenerative disorders termed synucleinopathies, including Parkinson's disease (PD). Mouse aSyn contains a threonine residue at position 53 that mimics the human familial PD substitution A53T, yet in contrast to A53T patients, mice show no evidence of aSyn neuropathology even after aging. Here, we studied the neurotoxicity of human A53T, mouse aSyn, and various human-mouse chimeras in cellular and in vivo models, as well as their biochemical properties relevant to aSyn pathobiology.

METHODS

Primary midbrain cultures transduced with aSyn-encoding adenoviruses were analyzed immunocytochemically to determine relative dopaminergic neuron viability. Brain sections prepared from rats injected intranigrally with aSyn-encoding adeno-associated viruses were analyzed immunohistochemically to determine nigral dopaminergic neuron viability and striatal dopaminergic terminal density. Recombinant aSyn variants were characterized in terms of fibrillization rates by measuring thioflavin T fluorescence, fibril morphologies via electron microscopy and atomic force microscopy, and protein-lipid interactions by monitoring membrane-induced aSyn aggregation and aSyn-mediated vesicle disruption. Statistical tests consisted of ANOVA followed by Tukey's multiple comparisons post hoc test and the Kruskal-Wallis test followed by a Dunn's multiple comparisons test or a two-tailed Mann-Whitney test.

RESULTS

Mouse aSyn was less neurotoxic than human aSyn A53T in cell culture and in rat midbrain, and data obtained for the chimeric variants indicated that the human-to-mouse substitutions D121G and N122S were at least partially responsible for this decrease in neurotoxicity. Human aSyn A53T and a chimeric variant with the human residues D and N at positions 121 and 122 (respectively) showed a greater propensity to undergo membrane-induced aggregation and to elicit vesicle disruption. Differences in neurotoxicity among the human, mouse, and chimeric aSyn variants correlated weakly with differences in fibrillization rate or fibril morphology.

CONCLUSIONS

Mouse aSyn is less neurotoxic than the human A53T variant as a result of inhibitory effects of two C-terminal amino acid substitutions on membrane-induced aSyn aggregation and aSyn-mediated vesicle permeabilization. Our findings highlight the importance of membrane-induced self-assembly in aSyn neurotoxicity and suggest that inhibiting this process by targeting the C-terminal domain could slow neurodegeneration in PD and other synucleinopathy disorders.

An Introduction to Model Compounds of Lignin Linking Motifs; Synthesis and Selection Considerations for Reactivity Studies

The development of fundamentally new valorization strategies for lignin plays a vital role in unlocking the true potential of lignocellulosic biomass as sustainable and economically compatible renewable carbon feedstock. In particular, new catalytic modification and depolymerization strategies are required. Progress in this field, past and future, relies for a large part on the application of synthetic model compounds that reduce the complexity of working with the lignin biopolymer. This aids the development of catalytic methodologies and in-depth mechanistic studies and guides structural characterization studies in the lignin field. However, due to the volume of literature and the piecemeal publication of methodology, the choice of suitable lignin model compounds is far from straight forward, especially for those outside the field and lacking a background in organic synthesis. For example, in catalytic depolymerization studies, a balance between synthetic effort and fidelity compared to the actual lignin of interest needs to be found. In this Review, we provide a broad overview of the model compounds available to study the chemistry of the main native linking motifs typically found in lignins from woody biomass, the synthetic routes and effort required to access them, and discuss to what extent these represent actual lignin structures. This overview can aid researchers in their selection of the most suitable lignin model systems for the development of emerging lignin modification and depolymerization technologies, maximizing their chances of successfully developing novel lignin valorization strategies.

Functional diversity of habitat formers declines scale-dependently across an environmental stress gradient

Marine habitat formers such as seaweeds and corals are lynchpins of coastal ecosystems, but their functional diversity and how it varies with scale and context remains poorly studied. Here, we investigate the functional diversity of seaweed assemblages across the rocky intertidal stress gradient at large (zones) and small (quadrat) scales. We quantified complementary metrics of emergent group richness, functional richness (functional space occupied) and functional dispersion (trait complementarity of dominant species). With increasing shore height, under species loss and turnover, responses of functional diversity were scale- and metric-dependent. At the large scale, functional richness contracted while—notwithstanding a decline in redundancy—emergent group richness and functional dispersion were both invariant. At the small scale, all measures declined, with the strongest responses evident for functional and emergent group richness. Comparisons of observed versus expected values based on null models revealed that functional richness and dispersion were greater than expected in the low shore but converged with expected values higher on the shore. These results show that functional diversity of assemblages of marine habitat formers can be especially responsive to environmental stress gradients at small scales and for richness measures. Furthermore, niche-based processes at the small—neighbourhood—scale can favour co-occurrence of functionally distinctive species under low, but not high, stress, magnifying differences in functional diversity across environmental gradients. As assemblages of marine habitat formers face accelerating environmental change, further studies examining multiple aspects of functional diversity are needed to elucidate patterns, processes, and ecosystem consequences of community (dis-)assembly across diverse groups.

Light-Activated Carbon Monoxide Prodrugs Based on Bipyridyl Dicarbonyl Ruthenium(II) Complexes

Two photoactivatable dicarbonyl ruthenium(II) complexes based on an amide-functionalised bipyridine scaffold (4-position) equipped with an alkyne functionality or a green-fluorescent BODIPY (boron-dipyrromethene) dye have been prepared and used to investigate their light-induced decarbonylation. UV/Vis, FTIR and 13 C NMR spectroscopies as well as gas chromatography and multivariate curve resolution alternating least-squares analysis (MCR-ALS) were used to elucidate the mechanism of the decarbonylation process. Release of the first CO molecule occurs very quickly, while release of the second CO molecule proceeds more slowly. In vitro studies using two cell lines A431 (human squamous carcinoma) and HEK293 (human embryonic kidney cells) have been carried out in order to characterise the anti-proliferative and anti-apoptotic activities. The BODIPY-labelled compound allows for monitoring the cellular uptake, showing fast internalisation kinetics and accumulation at the endoplasmic reticulum and mitochondria.

Investigating the origin and consequences of endogenous default options in repeated economic choices

Classical value-based decision theories state that economic choices are solely based on the value of available options. Experimental evidence suggests, however, that individuals’ choices are biased towards default options, prompted by the framing of decisions. Although the effects of default options created by exogenous framing–such as how choice options are displayed–are well-documented, little is known about the potential effects and properties of endogenous framing, that is, originating from an individual's internal state. In this study, we investigated the existence and properties of endogenous default options in a task involving choices between risky lotteries. By manipulating and examining the effects of three experimental features–time pressure, time spent on task and relative choice proportion towards a specific option–, we reveal and dissociate two features of endogenous default options which bias individuals’ choices: a natural tendency to prefer certain types of options (natural default), and the tendency to implicitly learn a default option from past choices (learned default). Additional analyses suggest that while the natural default may bias the standard choice process towards an option category, the learned default effects may be attributable to a second independent choice process. Overall, these investigations provide a first experimental evidence of how individuals build and apply diverse endogenous default options in economic decision-making and how this biases their choices.

A synthetic glycan array containing Cryptococcus neoformans glucuronoxylomannan capsular polysaccharide fragments allows the mapping of protective epitopes

A convergent synthetic strategy to Cryptococcus neoformans glucuronoxylomannan (GXM) capsular polysaccharide part structures was developed based on di-, tri-, tetra-, penta- and hexasaccharide thioglycoside building blocks. The approach permitted the synthesis of a library of spacer-containing serotype A and D related GXM oligosaccharide structures, ranging from di- to octadecasaccharides. Ten deprotected GXM compounds (mono- to decasaccharide) were printed onto microarray plates and screened with seventeen mouse monoclonal antibodies (mAbs) to GXM. For the first time a GXM oligosaccharide structure (a serotype A decasaccharide), capable of being recognized by neutralizing forms of these GXM-specific mAbs, has been identified, offering insight into the binding epitopes of a range of protective monoclonal antibodies and furthering our efforts to develop semi-synthetic conjugate vaccine candidates against C. neoformans.

[FeFe]-hydrogenase maturation: H-cluster assembly intermediates tracked by electron paramagnetic resonance, infrared, and X-ray absorption spectroscopy

[FeFe]-hydrogenase enzymes employ a unique organometallic cofactor for efficient and reversible hydrogen conversion. This so-called H-cluster consists of a [4Fe-4S] cubane cysteine linked to a diiron complex coordinated by carbon monoxide and cyanide ligands and an azadithiolate ligand (adt = NH(CH2S)2)·[FeFe]-hydrogenase apo-protein binding only the [4Fe-4S] sub-complex can be fully activated in vitro by the addition of a synthetic diiron site precursor complex ([2Fe]adt). Elucidation of the mechanism of cofactor assembly will aid in the design of improved hydrogen processing synthetic catalysts. We combined electron paramagnetic resonance, Fourier-transform infrared, and X-ray absorption spectroscopy to characterize intermediates of H-cluster assembly as initiated by mixing of the apo-protein (HydA1) from the green alga Chlamydomonas reinhardtii with [2Fe]adt. The three methods consistently show rapid formation of a complete H-cluster in the oxidized, CO-inhibited state (Hox-CO) already within seconds after the mixing. Moreover, FTIR spectroscopy support a model in which Hox-CO formation is preceded by a short-lived Hred'-CO-like intermediate. Accumulation of Hox-CO was followed by CO release resulting in the slower conversion to the catalytically active state (Hox) as well as formation of reduced states of the H-cluster.

Mesocellular Silica Foams (MCFs) with Tunable Pore Size as a Support for Lysozyme Immobilization: Adsorption Equilibrium and Kinetics, Biocomposite Properties

The effect of the porous structure of mesocellular silica foams (MCFs) on the lysozyme (LYS) adsorption capacity, as well as the rate, was studied to design the effective sorbent for potential applications as the carriers of biomolecules. The structural (N2 adsorption/desorption isotherms), textural (SEM, TEM), acid-base (potentiometric titration), adsorption properties, and thermal characteristics of the obtained lysozyme/silica composites were studied. The protein adsorption equilibrium and kinetics showed significant dependence on silica pore size. For instance, LYS adsorption uptake on MCF-6.4 support (pore diameter 6.4 nm) was about 0.29 g/g. The equilibrium loading amount of LYS on MCF-14.5 material (pore size 14.5 nm) increased to 0.55 g/g. However, when the pore diameter was larger than 14.5 nm, the LYS adsorption value systematically decreased with increasing pore size (e.g., for MCF-30.1 was only 0.27 g/g). The electrostatic attractive interactions between the positively charged lysozyme (at pH = 7.4) and the negatively charged silica played a significant role in the immobilization process. The differences in protein adsorption and surface morphology for the biocomposites of various pore sizes were found. The thermal behavior of the studied bio/systems was conducted by TG/DSC/FTIR/MS coupled method. It was found that the thermal degradation of lysozyme/silica composites was a double-stage process in the temperature range 165-420-830 °C.

A lineage-tracing tool to map the fate of hypoxic tumour cells

Intratumoural hypoxia is a common characteristic of malignant treatment-resistant cancers. However, hypoxia-modification strategies for the clinic remain elusive. To date, little is known on the behaviour of individual hypoxic tumour cells in their microenvironment. To explore this issue in a spatial and temporally controlled manner, we developed a genetically encoded sensor by fusing the O2-labile hypoxia-inducible factor 1α (HIF-1α) protein to eGFP and a tamoxifen-regulated Cre recombinase. Under normoxic conditions, HIF-1α is degraded but, under hypoxia, the HIF-1α-GFP-Cre-ERT2 fusion protein is stabilised and in the presence of tamoxifen activates a tdTomato reporter gene that is constitutively expressed in hypoxic progeny. We visualise the random distribution of hypoxic tumour cells from hypoxic or necrotic regions and vascularised areas using immunofluorescence and intravital microscopy. Once tdTomato expression is induced, it is stable for at least 4 weeks. Using this system, we could show in vivo that the post-hypoxic cells were more proliferative than non-labelled cells. Our results demonstrate that single-cell lineage tracing of hypoxic tumour cells can allow visualisation of their behaviour in living tumours using intravital microscopy. This tool should prove valuable for the study of dissemination and treatment response of post-hypoxic tumour cells in vivo at single-cell resolution.This article has an associated First Person interview with the joint first authors of the paper.

The Anthropological and Ethnographic Approaches to Social Representations Theory - an Empirical Meta-Theoretical Analysis

Part of a larger project aimed at performing an empirical meta-theoretical analysis of the entire corpus of scientific literature on Social Representations Theory (SRT), this research presents the state of the art of the anthropological and ethnographic approaches to SRT. Applying the Grid for Meta-Theoretical Analysis on 295 publications selected from the So.Re.Com"A.S. de Rosa"@-library, we compiled a rich set of meta-data and data illustrative of how SRT was conceptualized and operationalized within the anthropological and ethnographic approaches, as well as its positioning among other theoretical and disciplinary frameworks. The data was submitted to textual analysis, followed by a Hierarchical Clustering on Principal Components analysis. The empirical results suggest that from a theoretical standpoint, the anthropological and ethnographic approaches - inspired by its main exponents Jodelet (1991, 2016) and Duveen and Lloyd, (1986, 1993) - are consistent with the dynamic conceptualization of social representations set out by Moscovici (1961/1976, 1984/2003, 1988, 2000, 2013), as revolutionary paradigm that has shifted the emphasis of social psychology from looking at isolated variables in individuals in the abstract, towards a supra-disciplinary integrative vision of a social science, that investigates the genesis, transformation and negotiation of social representations in the communicative actual contexts (Billig 1991; de Rosa 2013a, b; Sammut et al. 2015a). From an empirical perspective, the variety of qualitative methods employed were open to investigate socio-cultural dimensions and symbolic universes, reflecting the integrative tradition of SRT that bridges diverse neighbouring disciplines in an effort towards a multifaceted perspective on the object of study.

Polygenic analysis of very high acetic acid tolerance in the yeast Saccharomyces cerevisiae reveals a complex genetic background and several new causative alleles

BACKGROUND

High acetic acid tolerance is of major importance in industrial yeast strains used for second-generation bioethanol production, because of the high acetic acid content of lignocellulose hydrolysates. It is also important in first-generation starch hydrolysates and in sourdoughs containing significant acetic acid levels. We have previously identified snf4 ^E269* as a causative allele in strain MS164 obtained after whole-genome (WG) transformation and selection for improved acetic acid tolerance.

RESULTS

We have now performed polygenic analysis with the same WG transformant MS164 to identify novel causative alleles interacting with snf4 ^E269* to further enhance acetic acid tolerance, from a range of 0.8-1.2% acetic acid at pH 4.7, to previously unmatched levels for Saccharomyces cerevisiae. For that purpose, we crossed the WG transformant with strain 16D, a previously identified strain displaying very high acetic acid tolerance. Quantitative trait locus (QTL) mapping with pooled-segregant whole-genome sequence analysis identified four major and two minor QTLs. In addition to confirmation of snf4 ^E269* in QTL1, we identified six other genes linked to very high acetic acid tolerance, TRT2, MET4, IRA2 and RTG1 and a combination of MSH2 and HAL9, some of which have never been connected previously to acetic acid tolerance. Several of these genes appear to be wild-type alleles that complement defective alleles present in the other parent strain.

CONCLUSIONS

The presence of several novel causative genes highlights the distinct genetic basis and the strong genetic background dependency of very high acetic acid tolerance. Our results suggest that elimination of inferior mutant alleles might be equally important for reaching very high acetic acid tolerance as introduction of rare superior alleles. The superior alleles of MET4 and RTG1 might be useful for further improvement of acetic acid tolerance in specific industrial yeast strains.

Guest Binding Drives Host Redistribution in Libraries of CoII 4 L4 Cages

Two CoII 4 L4 tetrahedral cages prepared from similar building blocks showed contrasting host-guest properties. One cage did not bind guests, whereas the second encapsulated a series of anions, due to electronic and geometric effects. When the building blocks of both cages were present during self-assembly, a library of five CoII LA x LB 4-x cages was formed in a statistical ratio in the absence of guests. Upon incorporation of anions able to interact preferentially with some library members, the products obtained were redistributed in favor of the best anion binders. To quantify the magnitudes of these templation effects, ESI-MS was used to gauge the effect of each template upon library redistribution.

Paradoxical activation of AMPK by glucose drives selective EP300 activity in colorectal cancer

Coordination of gene expression with nutrient availability supports proliferation and homeostasis and is shaped by protein acetylation. Yet how physiological/pathological signals link acetylation to specific gene expression programs and whether such responses are cell-type–specific is unclear. AMP-activated protein kinase (AMPK) is a key energy sensor, activated by glucose limitation to resolve nutrient supply–demand imbalances, critical for diabetes and cancer. Unexpectedly, we show here that, in gastrointestinal cancer cells, glucose activates AMPK to selectively induce EP300, but not CREB-binding protein (CBP). Consequently, EP300 is redirected away from nuclear receptors that promote differentiation towards β-catenin, a driver of proliferation and colorectal tumorigenesis. Importantly, blocking glycogen synthesis permits reactive oxygen species (ROS) accumulation and AMPK activation in response to glucose in previously nonresponsive cells. Notably, glycogen content and activity of the ROS/AMPK/EP300/β-catenin axis are opposite in healthy versus tumor sections. Glycogen content reduction from healthy to tumor tissue may explain AMPK switching from tumor suppressor to activator during tumor evolution.

Metabolic context determines whether the key energy sensor AMPK is a tumor suppressor or tumor promoter. This paradoxical behavior is explained through glucose inhibition of AMPK in healthy tissue versus glucose induction of AMPK in cancer colon epithelial cells.

Dual catalytic enantioselective desymmetrization of allene-tethered cyclohexanones

The construction of enantioenriched azabicyclo[3.3.1]nonan-6-one heterocycles via an enantioselective desymmetrization of allene-linked cyclohexanones, enabled through a dual catalytic system, that provides synchronous activation of the cyclohexanone with a chiral prolinamide and the allene with a copper(i) co-catalyst to deliver the stereodefined bicyclic core, is described. Successful application to oxygen analogues was also achieved, thereby providing a new enantioselective synthetic entry to architecturally complex bicyclic ethereal frameworks. The mechanistic pathway and the origin of enantio- and diastereoselectivities has been uncovered using density functional theory (DFT) calculations.

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency.

Finding Phrases: The Interplay of Word Frequency, Phrasal Prosody and Co-speech Visual Information in Chunking Speech by Monolingual and Bilingual Adults

The audiovisual speech signal contains multimodal information to phrase boundaries. In three artificial language learning studies with 12 groups of adult participants we investigated whether English monolinguals and bilingual speakers of English and a language with opposite basic word order (i.e., in which objects precede verbs) can use word frequency, phrasal prosody and co-speech (facial) visual information, namely head nods, to parse unknown languages into phrase-like units. We showed that monolinguals and bilinguals used the auditory and visual sources of information to chunk "phrases" from the input. These results suggest that speech segmentation is a bimodal process, though the influence of co-speech facial gestures is rather limited and linked to the presence of auditory prosody. Importantly, a pragmatic factor, namely the language of the context, seems to determine the bilinguals' segmentation, overriding the auditory and visual cues and revealing a factor that begs further exploration.

Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism

Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.

Spectral contrast effects are modulated by selective attention in "cocktail party" settings

Speech sounds are perceived relative to spectral properties of surrounding speech. For instance, target words that are ambiguous between /bɪt/ (with low F1) and /bɛt/ (with high F1) are more likely to be perceived as "bet" after a "low F1" sentence, but as "bit" after a "high F1" sentence. However, it is unclear how these spectral contrast effects (SCEs) operate in multi-talker listening conditions. Recently, Feng and Oxenham (J.Exp.Psychol.-Hum.Percept.Perform. 44(9), 1447-1457, 2018b) reported that selective attention affected SCEs to a small degree, using two simultaneously presented sentences produced by a single talker. The present study assessed the role of selective attention in more naturalistic "cocktail party" settings, with 200 lexically unique sentences, 20 target words, and different talkers. Results indicate that selective attention to one talker in one ear (while ignoring another talker in the other ear) modulates SCEs in such a way that only the spectral properties of the attended talker influences target perception. However, SCEs were much smaller in multi-talker settings (Experiment 2) than those in single-talker settings (Experiment 1). Therefore, the influence of SCEs on speech comprehension in more naturalistic settings (i.e., with competing talkers) may be smaller than estimated based on studies without competing talkers.

Examination of the ocean as a source for atmospheric microplastics

Global plastic litter pollution has been increasing alongside demand since plastic products gained commercial popularity in the 1930's. Current plastic pollutant research has generally assumed that once plastics enter the ocean they are there to stay, retained permanently within the ocean currents, biota or sediment until eventual deposition on the sea floor or become washed up onto the beach. In contrast to this, we suggest it appears that some plastic particles could be leaving the sea and entering the atmosphere along with sea salt, bacteria, virus' and algae. This occurs via the process of bubble burst ejection and wave action, for example from strong wind or sea state turbulence. In this manuscript we review evidence from the existing literature which is relevant to this theory and follow this with a pilot study which analyses microplastics (MP) in sea spray. Here we show first evidence of MP particles, analysed by μRaman, in marine boundary layer air samples on the French Atlantic coast during both onshore (average of 2.9MP/m3) and offshore (average of 9.6MP/m3) winds. Notably, during sampling, the convergence of sea breeze meant our samples were dominated by sea spray, increasing our capacity to sample MPs if they were released from the sea. Our results indicate a potential for MPs to be released from the marine environment into the atmosphere by sea-spray giving a globally extrapolated figure of 136000 ton/yr blowing on shore.

ERCC1-XPF targeting to psoralen-DNA crosslinks depends on XPA and FANCD2

The effectiveness of many DNA-damaging chemotherapeutic drugs depends on their ability to form monoadducts, intrastrand crosslinks and/or interstrand crosslinks (ICLs) that interfere with transcription and replication. The ERCC1-XPF endonuclease plays a critical role in removal of these lesions by incising DNA either as part of nucleotide excision repair (NER) or interstrand crosslink repair (ICLR). Engagement of ERCC1-XPF in NER is well characterized and is facilitated by binding to the XPA protein. However, ERCC1-XPF recruitment to ICLs is less well understood. Moreover, specific mutations in XPF have been found to disrupt its function in ICLR but not in NER, but whether this involves differences in lesion targeting is unknown. Here, we imaged GFP-tagged ERCC1, XPF and ICLR-defective XPF mutants to investigate how in human cells ERCC1-XPF is localized to different types of psoralen-induced DNA lesions, repaired by either NER or ICLR. Our results confirm its dependence on XPA in NER and furthermore show that its engagement in ICLR is dependent on FANCD2. Interestingly, we find that two ICLR-defective XPF mutants (R689S and S786F) are less well recruited to ICLs. These studies highlight the differential mechanisms that regulate ERCC1-XPF activity in DNA repair.

Parametric emulation and inference in computationally expensive integrated urban water quality simulators

Water quality environmental assessment often requires the joint simulation of several subsystems (e.g. wastewater treatment processes, urban drainage and receiving water bodies). The complexity of these integrated catchment models grows fast, leading to potentially over-parameterised and computationally expensive models. The receiving water body physical and biochemical parameters are often a dominant source of uncertainty when simulating dissolved oxygen depletion processes. Thus, the use of system observations to refine prior knowledge (from experts or literature) is usually required. Unfortunately, simulating real-world scale water quality processes results in a significant computational burden, for which the use of sampling intensive applications (e.g. parametric inference) is severely hampered. Data-driven emulation aims at creating an interpolation map between the parametric and output multidimensional spaces of a dynamic simulator, thus providing a fast approximation of the model response. In this study a large-scale integrated urban water quality model is used to simulate dissolved oxygen depletion processes in a sensitive river. A polynomial expansion emulator was proposed to approximate the link between four and eight river physical and biochemical river parameters and the dynamics of river flow and dissolved oxygen concentration during one year (at hourly frequency). The emulator scheme was used to perform a sensitivity analysis and a formal parametric inference using local system observations. The effect of different likelihood assumptions (e.g. heteroscedasticity, normality and autocorrelation) during the inference of dissolved oxygen processes is also discussed. This study shows how the use of data-driven emulators can facilitate the integration of formal uncertainty analysis schemes in the hydrological and water quality modelling community.